Category: publications

Mechanical Properties from Periodic PlaneWave Quantum Mechanical Codes: The Challenge of the Flexible Nanoporous MIL-47(V) Framework

Authors: Danny E. P. Vanpoucke, Kurt Lejaeghere, Veronique Van Speybroeck, Michel Waroquier, and An
Journal: J. Phys. Chem. C 119(41), 23752-23766 (2015)
doi: 10.1021/acs.jpcc.5b06809
IF(2015): 4.509
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pdf: <J.Phys.Chem.C> 
Graphical Abstract: Pulay stresses complicate the structure optimization of the breathing MIL-47(V) Metal-Organic Framework.
Graphical Abstract: Pulay stresses complicate the structure optimization of the breathing MIL-47(V) Metal-Organic Framework.


Modeling the flexibility of metal–organic frameworks (MOFs) requires the computation of mechanical properties from first principles, e.g., for screening of materials in a database, for gaining insight into structural transformations, and for force field development. However, this paper shows that computations with periodic density functional theory are challenged by the flexibility of these materials: guidelines from experience with standard solid-state calculations cannot be simply transferred to flexible porous frameworks. Our test case, the MIL-47(V) material, has a large-pore and a narrow-pore shape. The effect of Pulay stress (cf. Pulay forces) leads to drastic errors for a simple structure optimization of the flexible MIL-47(V) material. Pulay stress is an artificial stress that tends to lower the volume and is caused by the finite size of the plane wave basis set. We have investigated the importance of this Pulay stress, of symmetry breaking, and of k-point sampling on (a) the structure optimization and (b) mechanical properties such as elastic constants and bulk modulus, of both the large-pore and narrow-pore structure of MIL-47(V). We found that, in the structure optimization, Pulay effects should be avoided by using a fitting procedure, in which an equation of state E(V) (EOS) is fit to a series of energy versus volume points. Manual symmetry breaking could successfully lower the energy of MIL-47(V) by distorting the vanadium–oxide distances in the vanadyl chains and by rotating the benzene linkers. For the mechanical properties, the curvature of the EOS curve was compared with the Reuss bulk modulus, derived from the elastic tensor in the harmonic approximation. Errors induced by anharmonicity, the eggbox effect, and Pulay effects propagate into the Reuss modulus. The strong coupling of the unit cell axes when the unit cell deforms expresses itself in numerical instability of the Reuss modulus. For a flexible material, it is therefore advisible to resort to the EOS fit procedure.

Fine-tuning the theoretically predicted structure of MIL-47(V) with the aid of powder X-ray diffraction

Authors: Thomas Bogaerts, Louis Vanduyfhuys, Danny E. P. Vanpoucke, Jelle Wieme,
Michel Waroquier, Pascal van der Voort and Veronique van Speybroeck
Journal: Cryst. Eng. Comm. 17(45), 8612-8622 (2015)
doi: 10.1039/c5ce01388g
IF(2015): 3.849
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pdf: <Cryst.Eng.Comm.> 
Graphical Abstract: Which model represents the experimental XRD-spectra best? Ferromagnetic or anti-ferromagnetic chains? With of without offset?
Graphical Abstract: Which model represents the experimental XRD-spectra best? Ferromagnetic or anti-ferromagnetic chains? With of without offset?


The structural characterization of complex crystalline materials such as metal organic frameworks can prove a very difficult challenge both for experimentalists as for theoreticians. From theory, the flat potential energy surface of these highly flexible structures often leads to different geometries that are energetically very close to each other. In this work a distinction between various computationally determined structures is made by comparing experimental and theoretically derived X-ray diffractograms which are produced from the materials geometry. The presented approach allows to choose the most appropriate geometry of a MIL-47(V) MOF and even distinguish between different electronic configurations that induce small structural changes. Moreover the techniques presented here are used to verify the applicability of a newly developed force field for this material. The discussed methodology is of significant importance for modelling studies where accurate geometries are crucial, such as mechanical properties and adsorption of guest molecules.

Convergence of Atomic Charges with the Size of the Enzymatic Environment

Authors: Danny E. P. Vanpoucke, Julianna Oláh, Frank De Proft, Veronique Van Speybroeck, and Goedele Roos
Journal: J. Chem. Inf. Model. 55(3), 564-571 (2015)
doi: 10.1021/ci5006417
IF(2015): 3.657
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pdf: <J.Chem.Inf.Model.> 
Graphical Abstract: The influence of the cluster size and water presence on the atomic charge of active and inactive sites in Biomolecules.
Graphical Abstract: Graphical Abstract: The influence of the cluster size and water presence on the atomic charge of active and inactive sites in Bio-molecules.


Atomic charges are a key concept to give more insight into the electronic structure and chemical reactivity. The Hirshfeld-I partitioning scheme applied to the model protein human 2-cysteine peroxiredoxin thioredoxin peroxidase B is used to investigate how large a protein fragment needs to be in order to achieve convergence of the atomic charge of both, neutral and negatively charged residues. Convergence in atomic charges is rapidly reached for neutral residues, but not for negatively charged ones. This study pinpoints difficulties on the road towards accurate modeling of negatively charged residues of large bio-molecular systems in a multiscale approach.

Comment on ‘Europium doping induced symmetry deviation and its impact on the second harmonic generation of doped ZnO nanowires’

Authors: Danny E. P. Vanpoucke
Journal: Nanotechnology 25(45), 458001 (2014)
doi: 10.1088/0957-4484/25/45/458001
IF(2014): 3.821
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pdf: <Nanotechnology>


In Dhara et al. 2014 Nanotechnology 25 225202, the authors reported on the synthesis of Eu-doped ZnO nanowires (NWs) and investigated the influence of Eu doping on the second harmonic generation (SHG). Maximum SHG was found to correlate strongly with the structural deformation attributed to Eu3+ doping. In this comment, we show the deformation of interest is due to the presence of Eu2+ dopants, based on both the experimental data presented by Dhara et al. and ab-initio density functional theory calculations.

Quasi-1D physics in metal-organic frameworks: MIL-47(V) from first principles

Authors: Danny E. P. Vanpoucke, Jan W. Jaeken, Stijn De Baerdemacker, Kurt Lejaeghere
and Veronique Van Speybroeck
Journal: Beilstein J. Nanotechnol. 5, 1738-1748 (2014)
doi: 10.3762/bjnano.5.184
IF(2014): 2.670
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pdf: <Beilstein> (open access)
Graphical Abstract: (left) Spin density of anti-ferromagnetic MIL-47(V) with ferromagnetic chains. (right) Electronic band structure and density of states.
Graphical Abstract: The MIL-47(V) MOF has one unpaired electron per V site. As a result, different spin configurations are possible, several of which lead to an anti-ferromagnetic state. The spin density of an antiferromagnetic state, containing only ferromagnetic chains is shown on the left. On the right, the electronic band structure of the same system is presented.


The geometric and electronic structure of the MIL-47(V) metal-organic framework (MOF) is investigated by using ab initio density functional theory (DFT) calculations. Special focus is placed on the relation between the spin configuration and the properties of the MOF. The ground state is found to be antiferromagnetic, with an equilibrium volume of 1554.70 Å3. The transition pressure of the pressure-induced large-pore-to-narrow-pore phase transition is calculated to be 82 MPa and 124 MPa for systems with ferromagnetic and antiferromagnetic chains, respectively. For a mixed system, the transition pressure is found to be a weighted average of the ferromagnetic and antiferromagnetic transition pressures. Mapping DFT energies onto a simple-spin Hamiltonian shows both the intra- and inter-chain coupling to be antiferromagnetic, with the latter coupling constant being two orders of magnitude smaller than the former, suggesting the MIL-47(V) to present quasi-1D behavior. The electronic structure of the different spin configurations is investigated and it shows that the band gap position varies strongly with the spin configuration. The valence and conduction bands show a clear V d-character. In addition, these bands are flat in directions orthogonal to VO6 chains, while showing dispersion along the the direction of the VO6 chains, similar as for other quasi-1D materials.

Aliovalent Doping of CeO2: DFT study of oxidation state and vacancy effects

Authors: Danny E. P. Vanpoucke, Patrick Bultinck, Stefaan Cottenier, Veronique Van Speybroeck, and Isabel Van Driessche,
Journal: J. Mater. Chem. A 2(33), 13723-13737 (2014)
doi: 10.1039/C4TA02449D
IF(2014): 7.443
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pdf: <JMaterChemA> <arXiv>


The modification of CeO2 properties by means of aliovalent doping is investigated within the ab initio density functional theory framework. Lattice parameters, dopant atomic radii, bulk moduli and thermal expansion coefficients of fluorite type Ce1-xMxO2-y (with M = Mg, V, Co, Cu, Zn, Nb, Ba, La, Sm, Gd, Yb, and Bi) are presented for 0.00 ≤ x ≤ 0.25. The relative stability of the doped systems is discussed, and the influence of oxygen vacancies is investigated. It is shown that oxygen vacancies tend to increase the lattice parameter, and strongly decrease the bulk modulus. Defect formation energies are correlated with calculated crystal radii and covalent radii of the dopants, and are shown to present no simple trend. The previously observed inverse relationship between the thermal expansion coefficient and the bulk modulus in group IV doped CeO2 [J. Am. Ceram. Soc. 97(1), 258 (2014)] is shown to persist independent of the inclusion of charge compensating vacancies.

Tetravalent Doping of CeO2: The impact of valence electron character on group IV dopant influence

Authors: Danny E. P. Vanpoucke, Stefaan Cottenier, Veronique Van Speybroeck, Isabel Van Driessche, and Patrick Bultinck
Journal: J. Am. Ceram. Soc. 97(1), 258-266 (2014)
doi: 10.1111/jace.12650
IF(2014): 2.610
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pdf: <J.Am.Ceram.Soc.> <arXiv>


Fluorite CeO2 doped with group IV elements is studied within the density functional theory (DFT) and DFT + U framework. Concentration-dependent formation energies are calculated for Ce1−xZxO2 (Z = C, Si, Ge, Sn, Pb, Ti, Zr, Hf) with 0 ≤ x ≤ 0.25 and a roughly decreasing trend with ionic radius is observed. The influence of the valence and near valence electronic configuration is discussed, indicating the importance of filled d and f shells near the Fermi level for all properties investigated. A clearly different behavior of group IVa and IVb dopants is observed: the former are more suitable for surface modifications and the latter are more suitable for bulk modifications. For the entire set of group IV dopants, there exists an inverse relation between the change, due to doping, of the bulk modulus, and the thermal expansion coefficients. Hirshfeld-I atomic charges show that charge-transfer effects due to doping are limited to the nearest-neighbor oxygen atoms.

Modeling 1D structures on semiconductor surfaces: Synergy of theory and experiment

Authors: Danny E. P. Vanpoucke
Journal: J. Phys.: Condens. Matter 26(13), 133001 (2014)
doi: 10.1088/0953-8984/26/13/133001
IF(2014): 2.346
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pdf: <J.Phys.Condens.Matter> <arXiv>


Atomic scale nanowires attract enormous interest in a wide range of fields. On the one hand, due to their quasi-one-dimensional nature, they can act as an experimental testbed for exotic physics: Peierls instability, charge density waves, and Luttinger liquid behavior. On the other hand, due to their small size, they are of interest not only for future device applications in the micro-electronics industry, but also for applications regarding molecular electronics. This versatile nature makes them interesting systems to produce and study, but their size and growth conditions push both experimental production and theoretical modeling to their limits. In this review, modeling of atomic scale nanowires on semiconductor surfaces is discussed, focusing on the interplay between theory and experiment. The current state of modeling efforts on Pt- and Au-induced nanowires on Ge(001) is presented, indicating their similarities and differences. Recently discovered nanowire systems (Ir, Co, Sr) on the Ge(001) surface are also touched upon. The importance of scanning tunneling microscopy as a tool for direct comparison of theoretical and experimental data is shown, as is the power of density functional theory as an atomistic simulation approach. It becomes clear that complementary strengths of theoretical and experimental investigations are required for successful modeling of the atomistic nanowires, due to their complexity.

Rationality: A Social-Epistemology Perspective

Authors: Sylvia Wenmackers, Danny E. P. Vanpoucke, and Igor Douven
Journal: Front. Psychol. 5, 581 (2014)
doi: 10.3389/fpsyg.2014.00581
IF(2014): 2.560
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pdf: <Front.Psychol.> (open Access)


Both in philosophy and in psychology, human rationality has traditionally been studied from an ‘individualistic’ perspective. Recently, social epistemologists have drawn attention to the fact that epistemic interactions among agents also give rise to important questions concerning rationality. In previous work, we have used a formal model to assess the risk that a particular type of social-epistemic interactions lead agents with initially consistent belief states into inconsistent belief states. Here, we continue this work by investigating the dynamics to which these interactions may give rise in the population as a whole.

Cover Image of Journal of Computational Chemistry : Extending Hirshfeld-I

Authors: Danny E. P. Vanpoucke
Journal: J. Comput. Chem. 34(5), i-ii (2013)
doi: 10.1002/jcc.23239
IF(2013): 3.601
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pdf: <J.Comput.Chem.>


The image shows an isosurface of Hirshfeld-I “atoms in molecules” for Ti-doped CeO2, taken at an electron density of 0.03e/Å3, as presented by Danny E. P. Vanpoucke, Patrick Bultinck, and Isabel Van Driessche on page 405. The cubic Ce0.75Ti0.25O2 unit cell is shown along the 111 direction. The different atoms are still clearly distinguishable at this iso-surface level, and show the Ti atom in the corners to be much smaller than the Ce atoms on the sides. In this issue, this implementation of the Hirshfeld- I method for solids is published back to back with a Comment from Thomas A. Manz and the authors’ Reply.

Cover of Journal of Computational Chemistry: Volume 34, Issue 5, feb. 15, 2013